Installing wordpress multisite

Newbie here, I've put together many single user sites using fantastico on cpanel, so this is my first attempt at a multisite. I usually host my sites with hostgator but I figured I'd do this multisite project on a hosting account all to its own. So I have TMD hosting this project as I have used them before. They didn't have fantastico on their cpanel and so I had them install the wordpress multisite software. Then I started digging into the manuals here for installing wordpress multisite and now am wondering if I have to have their install cleaned off and start over due to file names they created and what the manuals are showing should be created in mysql ? Can I just add new files and leave their install files their?